Spring 2021
Three life domains: bacteria, archaea, and eukaryota
Your genome, along with your environment and experiences, shapes who you are
Physical traits tend to be strongly genetic
Each cell contains a complete copy of an organism’s genome, or blueprint for all cellular structures and activities
The genome is distributed along chromosomes, which are made of compressed and entwined DNA
Cells are of many different types (e.g. blood, skin, nerve cells), but all can be traced back to a single cell, the fertilized egg
The nucleus is a sub-compartment found only in eukaryotic cells, in which the organism’s DNA resides
The nuclear membrane separates the nucleus from the rest of the cell, which is called the cytoplasm
The entire cell is enclosed by the plasma membrane
Embedded within this membrane is a variety of protein structures that act as channels and pumps to control movement into and out of the cell
By the mid-1800s, microscopes were powerful enough to observe the presence of unusual structures called “chromosomes” that seemed to play an important role during cell division.
It was only possible to see the chromosomes unless appropriate stains were used
“Chromosome” comes from the Greek words meaning “color body”
Drawing of mitosis by Walther Flemming. Flemming, W. Zellsubstanz, Kern und Zelltheilung (F. C. W. Vogel, Leipzig, 1882).
Size. This is the easiest way to tell chromosomes apart
Banding pattern. The size and location of Giemsa bands make each chromosome unique
Centromere position. Centromeres appear as a constriction. They have a role in the separation of chromosomes into daughter cells during cell division (mitosis and meiosis)
Heterochromatic regions, which tend to be rich with adenine and thymine (AT-rich) DNA and relatively gene-poor, stain more darkly with Giemsa and result in G-banding
Less condensed (“open”) chromatin, which tends to be (GC-rich) and more transcriptionally active, incorporates less Giemsa stain, resulting in light bands in G-banding
Cytogenetic bands are labeled p1, p2, p3, q1, q2, q3, etc., counting from the centromere out toward the telomeres. At higher resolutions, sub-bands can be seen within the bands
For example, the locus for the CFTR (cystic fibrosis) gene is 7q31.2, which indicates it is on chromosome 7, q arm, band 3, sub-band 1, and sub-sub-band 2. (Say 7,q,3,1 dot 2)
The position of the centromere relative to the ends helps to tell chromosomes apart
The basic unit (nucleotide) is composed of an organic base attached to a deoxyribose sugar
The phosphate group also attached to the sugar
The base is one of cytosine (C), thymine (T), adenine (A), and guanine (G)
The information in DNA is stored as a code made up of four chemical bases: adenine (A), guanine (G), cytosine (C), and thymine (T)
The force that holds a base pair together is a weak hydrogen bond
Although each individual bond is weak, their cumulative effect along the strands is strong enough to bind the two strands tightly together
As a result, DNA is chemically inert and is a stable carrier of genetic information
Rules of base pairing: A-T(U), C-G
Genes are discrete hereditary units located on the chromosomes
Genes are segments of deoxyribonucleic acid (DNA) that contain the code for a specific protein that functions in one or more types of cells in the body
Genes contain information used to synthesize proteins, the building blocks of cells
Formulated by Francis Crick in 1956
DNA makes RNA and RNA makes protein
Transcription is the making of an RNA molecule off a DNA template
Translation is the making of a protein off an RNA template
RNA - ribonucleic acid:
DNA - deoxyribonucleic acid:
Messenger RNA (mRNA) - carrier of genetic information
Transfer RNA (tRNA) - deliver amino acids for protein synthesis
Ribosomal RNA (rRNA) - central component of ribosome, protein manufacturing machinery
Small RNA (siRNA, miRNA, snRNA, piwiRNA) - regulation of transcription/translation
The GT/AG mRNA processing rule is applicable for almost all eukaryotic genes
mRNA splicing - variants of mRNA assembly
Each cell contains a complete copy of the organism’s genome. A gene that is transcribed is said to be expressed
Not all cells express the same genes which is why different cells perform different functions
Even within the same cell different genes will be expressed at different times and perhaps at different levels
Housekeeping genes are genes that are required for the maintenance of basal cellular functions that are essential for the existence of a cell, regardless of its specific role in the tissue or organism
They are expected to be expressed in all cells of an organism under normal conditions, irrespective of tissue type, developmental stage, cell cycle state, or external signal
Can be used as internal controls in gene expression studies
3,804 housekeeping genes (and exons) defined from Human BodyMap project gene expression data http://www.tau.ac.il/~elieis/HKG/
Eisenberg, Eli, and Erez Y. Levanon. “Human Housekeeping Genes, Revisited.” Trends in Genetics: TIG 29, no. 10 (October 2013): 569–74. doi:10.1016/j.tig.2013.05.010.
Transcription factors (TFs) are proteins that bind to specific DNA sequences in the control region of each gene and determine whether or not the gene will be transcribed
The specific stretch of nucleotide sequence to which the TFs bind, often called a sequence motif, is usually quite short, typically 5-10 nucleotides long
Some TFs provide the RNA polymerase enzyme with access to the gene while other TFs block such access to ensure the gene is transcriptionally repressed
Computational biology attempts to use genome sequence to ascertain function of genes
Although genomes vary slightly from person to person, it seemed reasonable to try to establish a consensus human genome sequence
Robert Sinsheimer, chancellor of UC Santa Cruz, proposed to sequence the human genome in 1984
After much debate, the human genome project started in October 1990
Changes in DNA sequence/amount alter gene and/or protein product
Douglas Hanahan, Robert A. Weinberg. The Hallmarks of Cancer, Cell, 7 January 2000
The Polymerase chain reaction (PCR) enables one to make many copies of a particular DNA sequence anywhere in solution given only the starting/ending sequences (primers)
Developed in 1983 by Kary Mullis, PCR allows for the amplification of DNA fragments that are flanked by known “primer” sequences
Exquisitely sensitive and specific, it can amplify a single molecule in a sample into billions of copies with nearly perfect fidelity
Uses naturally occurring polymerase enzymes that copy DNA by adding free nucleotides to a single-stranded template
https://www.abmgood.com/marketing/knowledge_base/polymerase_chain_reaction_introduction.php
Cytogenetics is the study of normal and abnormal chromosomes
The normal configuration of chromosomes is often termed the euploid karyotypic state
Euploidy implies that each of the autosomes is present in normally structured pairs and that the X and Y chromosome are present in normally structured pairs for the sex of the individual
Deviation from the euploid karyotype - the state termed aneuploidy - is some alteration in the overall chromosome structure, such as loss of entire chromosomes, the presence of extra copies of chromosomes, etc.
http://vcell.ndsu.nodak.edu/animations/transcription/movie-flash.htm
In DNA replication, DNA polymerases unwind the DNA molecule by breaking the H-bonds between bases - strands separate
Once the polymerases have opened the molecule, an area known as the replication fork forms (always initiated at a certain set of nucleotides, the origin of replication)
New nucleotides are placed in the fork and link to the corresponding parental nucleotide already there (A with T, C with G)
